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I Need A List Of Bayesian Snp/Genotype Callers

Hi,

I need the first published method for Bayesian SNP/genotype calling and a list of all Bayesian SNP callers for next gen sequencing? It would also be hugely beneficial if there is a comparison paper or web site for these methods. Does any one have a handy list like that?

Thank you

snp genotyping next-gen sequencing
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updated by bgulko2 • bgulko2 • written by Biomed Biomed

5 answers

GigaBayes http://bioinformatics.bc.edu/marthlab/GigaBayes

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written by Marina Manrique Marina Manrique

Thanks Brad! It's cool that it operates on BAM files. And it seems they've moved to a MIT license

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written by Marina Manrique Marina Manrique

Two i can immediately think of:

BAMBINO: http://www.ncbi.nlm.nih.gov/pubmed/21278191 https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html

ComB: http://code.google.com/p/comb/. This requires read mapping using PerM and is SOLiD read based.

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written by Ian Ian

Comb is good in theory, but as it has not been published, though we do not know its practical performance.

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written by lh3 lh3

Comb is good in theory, but as it has not been published, so we do not know its practical performance

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written by lh3 lh3

Gabor's polybayes is the earliest I am aware of, although it is possible that there are earlier work. As to others:

  Atlas-SNP2 & Bayesian & Single & \citet{Shen:2010zr}\\
  CRISP & Testing$^2$ & Pooled$^3$ & \citet{Bansal:2010kx}\\
  Dindel$^4$ & HMM$^5$ & Pooled$^3$ & \citet{dindel}\\
  FreeBayes$^4$ & Bayesian & Multiple & http://github.com/ekg/freebayes\\
  GATK$^4$ & Bayesian & Multiple & \citet{McKenna:2010vn}\\
  glfMultiples$^4$ & Bayesian & Multiple & http://tinyurl.com/glfMultiples\\
  iCORN & Counting & Single & \citet{Otto:2010ly}\\
  MAQ & Bayesian & Single & \citet{Li:2008zr}\\
  QCALL$^4$ & Bayesian & Multiple & \citet{Le:2010bd} \\
  SAMtools$^4$ & Bayesian & Multiple & \citet{Li:2009ys}\\
  SeqEM & Bayesian & Multiple & \citet{Martin:2010dz}\\
  SliderII & Counting & Single & \citet{Malhis:2010qa}\\
  SNP-o-matic & Counting & Single & \citet{Manske:2009ve}\\
  SNPSeeker & LDT$^6$ & Pooled & \citet{Druley:2009vn}\\
  SNVMix2$^4$ & Bayesian & Single & \citet{Goya:2010mi}\\
  SOAPsnp & Bayesian & Single & \citet{Li:2009fu} \\
  SPLINTER & LDT$^6$ & Pooled & \citet{Vallania:2010ys}\\
  Syzygy$^4$ & Bayesian & Pooled$^3$ & http://tinyurl.com/syzygy-snp \\
  VARiD$^4$ & HMM$^3$ & Single & \citet{Dalca:2010rq} \\
  VarScan$^4$ & Counting & Pair$^6$ & \citet{Koboldt:2009fu}\\
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updated by Ram Ram • written by lh3 lh3

Thanks Heng. A very helpful list as usual. Do you think any of those stand out from the list as using a unique/radically different approach or unusual implementation etc.

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written by Biomed Biomed

Heng, FreeBayes is also capable of pooled detection.

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written by Erik Garrison Erik Garrison
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updated by Ram Ram • written by Brad Chapman Brad Chapman

Hi Brad, Do you know if Maq was the first published method to use bayesian genotype determination for next gen sequencing? Thanks

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written by Biomed Biomed

Heh, was going to say that Heng would know and it looks like he does. Deferring to that awesome answer.

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written by Brad Chapman Brad Chapman

We just released the BSNP Bayesian Genotype caller. It's been tested on Illumina, 454, SOLiD and Sanger human alignments ans has some technology specific bias correction. It requires a samtools pileup as input, but is fully Bayesian, considers both alignment and sequencing quality and doesn't bias towards the reference. If its helpful, have a look at:BSNP/GPhosCS Home Page

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updated by Ram Ram • written by bgulko2 • bgulko2

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